--- trunk/src/selection/SelectionManager.hpp	2005/02/01 06:55:00	277
+++ trunk/src/selection/SelectionManager.hpp	2015/01/09 19:06:35	2052
@@ -6,19 +6,10 @@
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,20 +28,315 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
+ * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
+ * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).          
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
 
 #ifndef SELECTION_SELECTIONMANAGER_HPP
 #define SELECTION_SELECTIONMANAGER_HPP
 
-namespace oopse {
+#include "selection/SelectionSet.hpp"
+#include "primitives/StuntDouble.hpp"
+#include "primitives/Bond.hpp"
+#include "primitives/Bend.hpp"
+#include "primitives/Torsion.hpp"
+#include "primitives/Inversion.hpp"
+#include "primitives/Molecule.hpp"
 
-/**
- * @class SelectionManager SelectionManager.hpp "selection/SelectionManager.hpp"
- * @brief
- */
-class SelectionManager {
+namespace OpenMD {
 
-};
+  class SimInfo;
+  class SelectionManager {
+  public:
+    SelectionManager(SimInfo* info);
 
+    void addSelection(StuntDouble* sd) {      
+      ss_.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
+    }
+    void addSelection(Bond* b) {
+      ss_.bitsets_[BOND].setBitOn(b->getGlobalIndex());
+    }
+    void addSelection(Bend* b) {
+      ss_.bitsets_[BEND].setBitOn(b->getGlobalIndex());
+    }
+    void addSelection(Torsion* t) {
+      ss_.bitsets_[TORSION].setBitOn(t->getGlobalIndex());
+    }
+    void addSelection(Inversion* i) {
+      ss_.bitsets_[INVERSION].setBitOn(i->getGlobalIndex());
+    }
+    void addSelection(Molecule* m) {
+      ss_.bitsets_[MOLECULE].setBitOn(m->getGlobalIndex());
+    }
+        
+    void addSelectionSet(const SelectionSet& bs) {
+      ss_.bitsets_[STUNTDOUBLE] |= bs.bitsets_[STUNTDOUBLE];
+    }
+    void addBondSelectionSet(const SelectionSet& bs) {
+      ss_.bitsets_[BOND] |= bs.bitsets_[BOND];
+    }
+    void addBendSelectionSet(const SelectionSet& bs) {
+      ss_.bitsets_[BEND] |= bs.bitsets_[BEND];
+    }
+    void addTorsionSelectionSet(const SelectionSet& bs) {
+      ss_.bitsets_[TORSION] |= bs.bitsets_[TORSION];
+    }
+    void addInversionSelectionSet(const SelectionSet& bs) {
+      ss_.bitsets_[INVERSION] |= bs.bitsets_[INVERSION];
+    }
+    void addMoleculeSelectionSet(const SelectionSet& bs) {
+      ss_.bitsets_[MOLECULE] |= bs.bitsets_[MOLECULE];
+    }
+
+    bool isEmpty() {
+      return ss_.bitsets_[STUNTDOUBLE].none() && ss_.bitsets_[BOND].none() 
+        && ss_.bitsets_[BEND].none()  && ss_.bitsets_[TORSION].none() 
+        && ss_.bitsets_[INVERSION].none() && ss_.bitsets_[MOLECULE].none();
+    }
+
+    void setSelectionSet(const SelectionSet& bs) {
+      for (int i = 0; i < N_SELECTIONTYPES; i++) 
+        ss_.bitsets_[i] = bs.bitsets_[i];
+    }
+
+    //void setSelectionSet(const SelectionSet& bs) {
+    //  ss_.bitsets_[STUNTDOUBLE] = bs.bitsets_[];           
+    //}
+    void setBondSelectionSet(const SelectionSet& bs) {
+      ss_.bitsets_[BOND] = bs.bitsets_[BOND];           
+    }
+    void setBendSelectionSet(const SelectionSet& bs) {
+      ss_.bitsets_[BEND] = bs.bitsets_[BEND];           
+    }
+    void setTorsionSelectionSet(const SelectionSet& bs) {
+      ss_.bitsets_[TORSION] = bs.bitsets_[TORSION];           
+    }
+    void setInversionSelectionSet(const SelectionSet& bs) {
+      ss_.bitsets_[INVERSION] = bs.bitsets_[INVERSION];           
+    }
+    void setMoleculeSelectionSet(const SelectionSet& bs) {
+      ss_.bitsets_[MOLECULE] = bs.bitsets_[MOLECULE];           
+    }
+
+    std::vector<int> getSelectionCounts() {
+      std::vector<int> counts(N_SELECTIONTYPES,0);
+      for (int i = 0; i < N_SELECTIONTYPES; i++) {
+        counts[i] = ss_.bitsets_[i].countBits();
+      }
+      return counts;
+    }
+     
+    int getSelectionCount() {
+      return ss_.bitsets_[STUNTDOUBLE].countBits();
+    }
+    int getBondSelectionCount() {
+      return ss_.bitsets_[BOND].countBits();
+    }
+    int getBendSelectionCount() {
+      return ss_.bitsets_[BEND].countBits();
+    }
+    int getTorsionSelectionCount() {
+      return ss_.bitsets_[TORSION].countBits();
+    }
+    int getInversionSelectionCount() {
+      return ss_.bitsets_[INVERSION].countBits();
+    }
+    int getMoleculeSelectionCount() {
+      return ss_.bitsets_[MOLECULE].countBits();
+    }
+    
+    SelectionSet getSelectionSet() {
+      return ss_;
+    }
+    /*    SelectionSet getBondSelectionSet() {
+      return ss_.bitsets_[BOND];
+    }
+    SelectionSet getBendSelectionSet() {
+      return ss_.bitsets_[BEND];
+    }
+    SelectionSet getTorsionSelectionSet() {
+      return ss_.bitsets_[TORSION];
+    }
+    SelectionSet getInversionSelectionSet() {
+      return ss_.bitsets_[INVERSION];
+    }
+    */
+
+    void setSelection(StuntDouble* sd) {
+      ss_.bitsets_[STUNTDOUBLE].clearAll();
+      ss_.bitsets_[STUNTDOUBLE].setBitOn(sd->getGlobalIndex());
+    }
+    void setSelection(Bond* b) {
+      ss_.bitsets_[BOND].clearAll();
+      ss_.bitsets_[BOND].setBitOn(b->getGlobalIndex());
+    }
+    void setSelection(Bend* b) {
+      ss_.bitsets_[BEND].clearAll();
+      ss_.bitsets_[BEND].setBitOn(b->getGlobalIndex());
+    }
+    void setSelection(Torsion* t) {
+      ss_.bitsets_[TORSION].clearAll();
+      ss_.bitsets_[TORSION].setBitOn(t->getGlobalIndex());
+    }
+    void setSelection(Inversion* i) {
+      ss_.bitsets_[INVERSION].clearAll();
+      ss_.bitsets_[INVERSION].setBitOn(i->getGlobalIndex());
+    }
+    void setSelection(Molecule* m) {
+      ss_.bitsets_[MOLECULE].clearAll();
+      ss_.bitsets_[MOLECULE].setBitOn(m->getGlobalIndex());
+    }
+
+    void toggleSelection(StuntDouble* sd) {
+      ss_.bitsets_[STUNTDOUBLE].flip(sd->getGlobalIndex());
+    }
+    void toggleSelection(Bond* b) {
+      ss_.bitsets_[BOND].flip(b->getGlobalIndex());
+    }
+    void toggleSelection(Bend* b) {
+      ss_.bitsets_[BEND].flip(b->getGlobalIndex());
+    }
+    void toggleSelection(Torsion* t) {
+      ss_.bitsets_[TORSION].flip(t->getGlobalIndex());
+    }
+    void toggleSelection(Inversion* i) {
+      ss_.bitsets_[INVERSION].flip(i->getGlobalIndex());
+    }
+    void toggleSelection(Molecule* m) {
+      ss_.bitsets_[MOLECULE].flip(m->getGlobalIndex());
+    }
+
+    void toggleSelection() {
+      for (int i = 0; i < N_SELECTIONTYPES; i++) 
+        ss_.bitsets_[i].flip();
+    }
+        
+    void selectAll() {
+      for (int i = 0; i < N_SELECTIONTYPES; i++) 
+        ss_.bitsets_[i].setAll();
+    }
+
+    void clearSelection() {
+      for (int i = 0; i < N_SELECTIONTYPES; i++) 
+        ss_.bitsets_[i].clearAll();
+    }
+
+    void clearSelection(StuntDouble* sd) {
+      ss_.bitsets_[STUNTDOUBLE].setBitOff(sd->getGlobalIndex());
+    }
+    void clearSelection(Bond* b) {
+      ss_.bitsets_[BOND].setBitOff(b->getGlobalIndex());
+    }
+    void clearSelection(Bend* b) {
+      ss_.bitsets_[BEND].setBitOff(b->getGlobalIndex());
+    }
+    void clearSelection(Torsion* t) {
+      ss_.bitsets_[TORSION].setBitOff(t->getGlobalIndex());
+    }
+    void clearSelection(Inversion* i) {
+      ss_.bitsets_[INVERSION].setBitOff(i->getGlobalIndex());
+    }
+    void clearSelection(Molecule* m) {
+      ss_.bitsets_[MOLECULE].setBitOff(m->getGlobalIndex());
+    }
+
+    bool isSelected(StuntDouble* sd) {
+      return ss_.bitsets_[STUNTDOUBLE][sd->getGlobalIndex()];
+    }
+    bool isSelected(Bond* b) {
+      return ss_.bitsets_[BOND][b->getGlobalIndex()];
+    }
+    bool isSelected(Bend* b) {
+      return ss_.bitsets_[BEND][b->getGlobalIndex()];
+    }
+    bool isSelected(Torsion* t) {
+      return ss_.bitsets_[TORSION][t->getGlobalIndex()];
+    }
+    bool isSelected(Inversion* i) {
+      return ss_.bitsets_[INVERSION][i->getGlobalIndex()];
+    }
+    bool isSelected(Molecule* m) {
+      return ss_.bitsets_[MOLECULE][m->getGlobalIndex()];
+    }
+
+    StuntDouble* beginSelected(int& i);
+    StuntDouble* nextSelected(int& i);
+    StuntDouble* beginUnselected(int& i);
+    StuntDouble* nextUnSelected(int& i);
+
+    Bond* beginSelectedBond(int& i);
+    Bond* nextSelectedBond(int& i);
+    Bond* beginUnselectedBond(int& i);
+    Bond* nextUnSelectedBond(int& i);
+
+    Bend* beginSelectedBend(int& i);
+    Bend* nextSelectedBend(int& i);
+    Bend* beginUnselectedBend(int& i);
+    Bend* nextUnSelectedBend(int& i);
+
+    Torsion* beginSelectedTorsion(int& i);
+    Torsion* nextSelectedTorsion(int& i);
+    Torsion* beginUnselectedTorsion(int& i);
+    Torsion* nextUnSelectedTorsion(int& i);
+
+    Inversion* beginSelectedInversion(int& i);
+    Inversion* nextSelectedInversion(int& i);
+    Inversion* beginUnselectedInversion(int& i);
+    Inversion* nextUnSelectedInversion(int& i);
+
+    Molecule* beginSelectedMolecule(int& i);
+    Molecule* nextSelectedMolecule(int& i);
+    Molecule* beginUnselectedMolecule(int& i);
+    Molecule* nextUnSelectedMolecule(int& i);
+
+    SelectionManager& operator&= (const SelectionManager &sman) {
+      for (int i = 0; i < N_SELECTIONTYPES; i++) 
+        ss_.bitsets_[i] &= sman.ss_.bitsets_[i];
+      return *this; 
+    }
+        
+    SelectionManager& operator|= (const SelectionManager &sman) {
+      for (int i = 0; i < N_SELECTIONTYPES; i++) 
+        ss_.bitsets_[i] |= sman.ss_.bitsets_[i];
+      return *this; 
+    }
+        
+    SelectionManager& operator^= (const SelectionManager &sman) {
+      for (int i = 0; i < N_SELECTIONTYPES; i++) 
+        ss_.bitsets_[i] ^= sman.ss_.bitsets_[i];
+      return *this; 
+    }
+
+    SelectionManager& operator-= (const SelectionManager &sman) {
+      for (int i = 0; i < N_SELECTIONTYPES; i++) 
+        ss_.bitsets_[i] -= sman.ss_.bitsets_[i];
+      return *this; 
+    }
+        
+    friend SelectionManager operator| (const SelectionManager& sman1, const SelectionManager& sman2);
+    friend SelectionManager operator& (const SelectionManager& sman1, const SelectionManager& sman2);
+    friend SelectionManager operator^ (const SelectionManager& sman1, const SelectionManager& sman2);
+    friend SelectionManager operator-(const SelectionManager& sman1, const SelectionManager& sman2);
+        
+  private:
+    SimInfo* info_;
+    SelectionSet ss_;
+    std::vector<int> nObjects_;
+    std::vector<StuntDouble*> stuntdoubles_;
+    std::vector<Bond*> bonds_;
+    std::vector<Bend*> bends_;
+    std::vector<Torsion*> torsions_;
+    std::vector<Inversion*> inversions_;
+    std::vector<Molecule*> molecules_;
+  };
+
 }
 #endif