src/brains/SimInfo.hpp

/*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * 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
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. 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.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * 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.
 */
 
/**
 * @file SimInfo.hpp
 * @author    tlin
 * @date  11/02/2004
 * @version 1.0
 */ 

#ifndef BRAINS_SIMMODEL_HPP
#define BRAINS_SIMMODEL_HPP

#include <iostream>
#include <set>
#include <utility>
#include <vector>

#include "brains/Exclude.hpp"
#include "io/Globals.hpp"
#include "math/Vector3.hpp"
#include "math/SquareMatrix3.hpp"
#include "types/MoleculeStamp.hpp"
#include "UseTheForce/ForceField.hpp"
#include "utils/PropertyMap.hpp"
#include "utils/LocalIndexManager.hpp"

//another nonsense macro declaration
#define __C
#include "brains/fSimulation.h"

namespace oopse{

  //forward decalration 
  class SnapshotManager;
  class Molecule;
  class SelectionManager;
  /**
   * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" 
   * @brief As one of the heavy weight class of OOPSE, SimInfo
   * One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
   * And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
   * cutoff groups, constrains).
   * Another major change is the index. No matter single version or parallel version,  atoms and
   * rigid bodies have both global index and local index. Local index is not important to molecule as well as
   * cutoff group. 
   */
  class SimInfo {
  public:
    typedef std::map<int, Molecule*>::iterator  MoleculeIterator;

    /**
     * Constructor of SimInfo
     * @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
     * second element is the total number of molecules with the same molecule stamp in the system
     * @param ff pointer of a concrete ForceField instance
     * @param simParams 
     * @note
     */
    SimInfo(ForceField* ff, Globals* simParams);
    virtual ~SimInfo();

    /**
     * Adds a molecule
     * @return return true if adding successfully, return false if the molecule is already in SimInfo
     * @param mol molecule to be added
     */
    bool addMolecule(Molecule* mol);

    /**
     * Removes a molecule from SimInfo
     * @return true if removing successfully, return false if molecule is not in this SimInfo
     */
    bool removeMolecule(Molecule* mol);

    /** Returns the total number of molecules in the system. */
    int getNGlobalMolecules() {
      return nGlobalMols_;
    }

    /** Returns the total number of atoms in the system. */
    int getNGlobalAtoms() {
      return nGlobalAtoms_;
    }

    /** Returns the total number of cutoff groups in the system. */
    int getNGlobalCutoffGroups() {
      return nGlobalCutoffGroups_;
    }

    /**
     * Returns the total number of integrable objects (total number of rigid bodies plus the total number
     * of atoms which do not belong to the rigid bodies) in the system
     */
    int getNGlobalIntegrableObjects() {
      return nGlobalIntegrableObjects_;
    }

    /**
     * Returns the total number of integrable objects (total number of rigid bodies plus the total number
     * of atoms which do not belong to the rigid bodies) in the system
     */
    int getNGlobalRigidBodies() {
      return nGlobalRigidBodies_;
    }

    int getNGlobalConstraints();
    /** 
     * Returns the number of local molecules.
     * @return the number of local molecules 
     */
    int getNMolecules() {
      return molecules_.size();
    }

    /** Returns the number of local atoms */
    unsigned int getNAtoms() {
      return nAtoms_;
    }

    /** Returns the number of local bonds */        
    unsigned int getNBonds(){
      return nBonds_;
    }

    /** Returns the number of local bends */        
    unsigned int getNBends() {
      return nBends_;
    }

    /** Returns the number of local torsions */        
    unsigned int getNTorsions() {
      return nTorsions_;
    }

    /** Returns the number of local rigid bodies */        
    unsigned int getNRigidBodies() {
      return nRigidBodies_;
    }

    /** Returns the number of local integrable objects */
    unsigned int getNIntegrableObjects() {
      return nIntegrableObjects_;
    }

    /** Returns the number of local cutoff groups */
    unsigned int getNCutoffGroups() {
      return nCutoffGroups_;
    }

    /** Returns the total number of constraints in this SimInfo */
    unsigned int getNConstraints() {
      return nConstraints_;
    }
        
    /**
     * Returns the first molecule in this SimInfo and intialize the iterator.
     * @return the first molecule, return NULL if there is not molecule in this SimInfo
     * @param i the iterator of molecule array (user shouldn't change it)
     */
    Molecule* beginMolecule(MoleculeIterator& i);

    /** 
     * Returns the next avaliable Molecule based on the iterator.
     * @return the next avaliable molecule, return NULL if reaching the end of the array 
     * @param i the iterator of molecule array
     */
    Molecule* nextMolecule(MoleculeIterator& i);

    /** Returns the number of degrees of freedom */
    int getNdf() {
      return ndf_;
    }

    /** Returns the number of raw degrees of freedom */
    int getNdfRaw() {
      return ndfRaw_;
    }

    /** Returns the number of translational degrees of freedom */
    int getNdfTrans() {
      return ndfTrans_;
    }

    //getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
        
    /** Returns the total number of z-constraint molecules in the system */
    int getNZconstraint() {
      return nZconstraint_;
    }

    /** 
     * Sets the number of z-constraint molecules in the system.
     */
    void setNZconstraint(int nZconstraint) {
      nZconstraint_ = nZconstraint;
    }
        
    /** Returns the snapshot manager. */
    SnapshotManager* getSnapshotManager() {
      return sman_;
    }

    /** Sets the snapshot manager. */
    void setSnapshotManager(SnapshotManager* sman);
        
    /** Returns the force field */
    ForceField* getForceField() {
      return forceField_;
    }

    Globals* getSimParams() {
      return simParams_;
    }

    /** Returns the velocity of center of mass of the whole system.*/
    Vector3d getComVel();

    /** Returns the center of the mass of the whole system.*/
    Vector3d getCom();
   /** Returns the center of the mass and Center of Mass velocity of the whole system.*/ 
    void getComAll(Vector3d& com,Vector3d& comVel);

    /** Returns intertia tensor for the entire system and system Angular Momentum.*/
    void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
    
    /** Returns system angular momentum */
    Vector3d getAngularMomentum();

    /** main driver function to interact with fortran during the initialization and molecule migration */
    void update();

    /** Returns the local index manager */
    LocalIndexManager* getLocalIndexManager() {
      return &localIndexMan_;
    }

    int getMoleculeStampId(int globalIndex) {
      //assert(globalIndex < molStampIds_.size())
      return molStampIds_[globalIndex];
    }

    /** Returns the molecule stamp */
    MoleculeStamp* getMoleculeStamp(int id) {
      return moleculeStamps_[id];
    }

    /** Return the total number of the molecule stamps */
    int getNMoleculeStamp() {
      return moleculeStamps_.size();
    }
    /**
     * Finds a molecule with a specified global index
     * @return a pointer point to found molecule
     * @param index
     */
    Molecule* getMoleculeByGlobalIndex(int index) {
      MoleculeIterator i;
      i = molecules_.find(index);

      return i != molecules_.end() ? i->second : NULL;
    }

    double getRcut() {
      return rcut_;
    }

    double getRsw() {
      return rsw_;
    }

    double getList() {
      return rlist_;
    }
        
    std::string getFinalConfigFileName() {
      return finalConfigFileName_;
    }
        
    void setFinalConfigFileName(const std::string& fileName) {
      finalConfigFileName_ = fileName;
    }

    std::string getDumpFileName() {
      return dumpFileName_;
    }
        
    void setDumpFileName(const std::string& fileName) {
      dumpFileName_ = fileName;
    }

    std::string getStatFileName() {
      return statFileName_;
    }
        
    void setStatFileName(const std::string& fileName) {
      statFileName_ = fileName;
    }
        
    std::string getRestFileName() {
      return restFileName_;
    }
        
    void setRestFileName(const std::string& fileName) {
      restFileName_ = fileName;
    }

    /** 
     * Sets GlobalGroupMembership
     * @see #SimCreator::setGlobalIndex
     */  
    void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
      assert(globalGroupMembership.size() == nGlobalAtoms_);
      globalGroupMembership_ = globalGroupMembership;
    }

    /** 
     * Sets GlobalMolMembership
     * @see #SimCreator::setGlobalIndex
     */        
    void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
      assert(globalMolMembership.size() == nGlobalAtoms_);
      globalMolMembership_ = globalMolMembership;
    }


    bool isFortranInitialized() {
      return fortranInitialized_;
    }
        
    //below functions are just forward functions
    //To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
    //the other hand, has-a relation need composing.
    /**
     * Adds property into property map
     * @param genData GenericData to be added into PropertyMap
     */
    void addProperty(GenericData* genData);

    /**
     * Removes property from PropertyMap by name
     * @param propName the name of property to be removed
     */
    void removeProperty(const std::string& propName);

    /**
     * clear all of the properties
     */
    void clearProperties();

    /**
     * Returns all names of properties
     * @return all names of properties
     */
    std::vector<std::string> getPropertyNames();

    /**
     * Returns all of the properties in PropertyMap
     * @return all of the properties in PropertyMap
     */      
    std::vector<GenericData*> getProperties();

    /**
     * Returns property 
     * @param propName name of property
     * @return a pointer point to property with propName. If no property named propName
     * exists, return NULL
     */      
    GenericData* getPropertyByName(const std::string& propName);

    /**
     * add all exclude pairs of a molecule into exclude list.
     */
    void addExcludePairs(Molecule* mol);

    /**
     * remove all exclude pairs which belong to a molecule from exclude list
     */

    void removeExcludePairs(Molecule* mol);


    /** Returns the unique atom types of local processor in an array */
    std::set<AtomType*> getUniqueAtomTypes();
        
    friend std::ostream& operator <<(std::ostream& o, SimInfo& info);

    void getCutoff(double& rcut, double& rsw);
        
  private:

    /** fill up the simtype struct*/
    void setupSimType();

    /**
     * Setup Fortran Simulation
     * @see #setupFortranParallel
     */
    void setupFortranSim();

    /** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
    void setupCutoff();

    /** Figure out which coulombic correction method to use and pass to fortran */
    void setupElectrostaticSummationMethod( int isError );

    /** Figure out which polynomial type to use for the switching function */
    void setupSwitchingFunction();

    /** Calculates the number of degress of freedom in the whole system */
    void calcNdf();
    void calcNdfRaw();
    void calcNdfTrans();

    ForceField* forceField_;      
    Globals* simParams_;

    std::map<int, Molecule*>  molecules_; /**< Molecule array */

    /**
     * Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
     * system.
     */
    void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
        
    //degress of freedom
    int ndf_;           /**< number of degress of freedom (excludes constraints),  ndf_ is local */
    int ndfRaw_;    /**< number of degress of freedom (includes constraints),  ndfRaw_ is local */
    int ndfTrans_; /**< number of translation degress of freedom, ndfTrans_ is local */
    int nZconstraint_; /** number of  z-constraint molecules, nZconstraint_ is global */
        
    //number of global objects
    int nGlobalMols_;       /**< number of molecules in the system */
    int nGlobalAtoms_;   /**< number of atoms in the system */
    int nGlobalCutoffGroups_; /**< number of cutoff groups in this system */
    int nGlobalIntegrableObjects_; /**< number of integrable objects in this system */
    int nGlobalRigidBodies_; /**< number of rigid bodies in this system */
    /**
     * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
     * corresponding content is the global index of cutoff group this atom belong to. 
     * It is filled by SimCreator once and only once, since it never changed during the simulation.
     */
    std::vector<int> globalGroupMembership_; 

    /**
     * the size of globalGroupMembership_  is nGlobalAtoms. Its index is  global index of an atom, and the
     * corresponding content is the global index of molecule this atom belong to. 
     * It is filled by SimCreator once and only once, since it is never changed during the simulation.
     */
    std::vector<int> globalMolMembership_;        

        
    std::vector<int> molStampIds_;                                /**< stamp id array of all molecules in the system */
    std::vector<MoleculeStamp*> moleculeStamps_;      /**< molecule stamps array */        
        
    //number of local objects
    int nAtoms_;                        /**< number of atoms in local processor */
    int nBonds_;                        /**< number of bonds in local processor */
    int nBends_;                        /**< number of bends in local processor */
    int nTorsions_;                    /**< number of torsions in local processor */
    int nRigidBodies_;              /**< number of rigid bodies in local processor */
    int nIntegrableObjects_;    /**< number of integrable objects in local processor */
    int nCutoffGroups_;             /**< number of cutoff groups in local processor */
    int nConstraints_;              /**< number of constraints in local processors */

    simtype fInfo_; /**< A dual struct shared by c++/fortran which indicates the atom types in simulation*/
    Exclude exclude_;      
    PropertyMap properties_;                  /**< Generic Property */
    SnapshotManager* sman_;               /**< SnapshotManager */

    /** 
     * The reason to have a local index manager is that when molecule is migrating to other processors, 
     * the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
     * information of molecule migrating to current processor, Migrator class can query  the LocalIndexManager
     * to make a efficient data moving plan.
     */        
    LocalIndexManager localIndexMan_;

    //file names
    std::string finalConfigFileName_;
    std::string dumpFileName_;
    std::string statFileName_;
    std::string restFileName_;
        
    double rcut_;       /**< cutoff radius*/
    double rsw_;        /**< radius of switching function*/
    double rlist_;      /**< neighbor list radius */

    bool fortranInitialized_; /**< flag indicate whether fortran side is initialized */

#ifdef IS_MPI
    //in Parallel version, we need MolToProc
  public:
                
    /**
     * Finds the processor where a molecule resides
     * @return the id of the processor which contains the molecule
     * @param globalIndex global Index of the molecule
     */
    int getMolToProc(int globalIndex) {
      //assert(globalIndex < molToProcMap_.size());
      return molToProcMap_[globalIndex];
    }

    /** 
     * Set MolToProcMap array
     * @see #SimCreator::divideMolecules
     */
    void setMolToProcMap(const std::vector<int>& molToProcMap) {
      molToProcMap_ = molToProcMap;
    }
        
  private:

    void setupFortranParallel();
        
    /** 
     * The size of molToProcMap_ is equal to total number of molecules in the system.
     *  It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
     * once.
     */        
    std::vector<int> molToProcMap_; 

#endif

  };

} //namespace oopse
#endif //BRAINS_SIMMODEL_HPP

Revision:	770
Committed:	Fri Dec 2 15:38:03 2005 UTC (19 years, 5 months ago) by tim
Original Path:	*trunk/src/brains/SimInfo.hpp*
File size:	18593 byte(s)
Log Message:	End of the Link --> List Return of the Oject-Oriented replace yacc/lex parser with antlr parser
#	User	Rev	Content
1	gezelter	507	/*
2	gezelter	246	* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			/**
43			* @file SimInfo.hpp
44			* @author tlin
45			* @date 11/02/2004
46			* @version 1.0
47			*/
48	gezelter	2
49	gezelter	246	#ifndef BRAINS_SIMMODEL_HPP
50			#define BRAINS_SIMMODEL_HPP
51
52			#include <iostream>
53			#include <set>
54			#include <utility>
55	gezelter	2	#include <vector>
56
57	tim	3	#include "brains/Exclude.hpp"
58	gezelter	246	#include "io/Globals.hpp"
59			#include "math/Vector3.hpp"
60	chuckv	555	#include "math/SquareMatrix3.hpp"
61	gezelter	246	#include "types/MoleculeStamp.hpp"
62			#include "UseTheForce/ForceField.hpp"
63			#include "utils/PropertyMap.hpp"
64			#include "utils/LocalIndexManager.hpp"
65	tim	316
66	gezelter	246	//another nonsense macro declaration
67	gezelter	2	#define __C
68	tim	3	#include "brains/fSimulation.h"
69	gezelter	2
70	gezelter	246	namespace oopse{
71	gezelter	2
72	gezelter	507	//forward decalration
73			class SnapshotManager;
74			class Molecule;
75			class SelectionManager;
76			/**
77			* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
78			* @brief As one of the heavy weight class of OOPSE, SimInfo
79			* One of the major changes in SimInfo class is the data struct. It only maintains a list of molecules.
80			* And the Molecule class will maintain all of the concrete objects (atoms, bond, bend, torsions, rigid bodies,
81			* cutoff groups, constrains).
82			* Another major change is the index. No matter single version or parallel version, atoms and
83			* rigid bodies have both global index and local index. Local index is not important to molecule as well as
84			* cutoff group.
85			*/
86			class SimInfo {
87			public:
88			typedef std::map<int, Molecule*>::iterator MoleculeIterator;
89	gezelter	2
90	gezelter	507	/**
91			* Constructor of SimInfo
92			* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
93			* second element is the total number of molecules with the same molecule stamp in the system
94			* @param ff pointer of a concrete ForceField instance
95			* @param simParams
96			* @note
97			*/
98	tim	770	SimInfo(ForceField* ff, Globals* simParams);
99	gezelter	507	virtual ~SimInfo();
100	gezelter	2
101	gezelter	507	/**
102			* Adds a molecule
103			* @return return true if adding successfully, return false if the molecule is already in SimInfo
104			* @param mol molecule to be added
105			*/
106			bool addMolecule(Molecule* mol);
107	gezelter	2
108	gezelter	507	/**
109			* Removes a molecule from SimInfo
110			* @return true if removing successfully, return false if molecule is not in this SimInfo
111			*/
112			bool removeMolecule(Molecule* mol);
113	gezelter	2
114	gezelter	507	/** Returns the total number of molecules in the system. */
115			int getNGlobalMolecules() {
116			return nGlobalMols_;
117			}
118	gezelter	2
119	gezelter	507	/** Returns the total number of atoms in the system. */
120			int getNGlobalAtoms() {
121			return nGlobalAtoms_;
122			}
123	gezelter	2
124	gezelter	507	/** Returns the total number of cutoff groups in the system. */
125			int getNGlobalCutoffGroups() {
126			return nGlobalCutoffGroups_;
127			}
128	gezelter	2
129	gezelter	507	/**
130			* Returns the total number of integrable objects (total number of rigid bodies plus the total number
131			* of atoms which do not belong to the rigid bodies) in the system
132			*/
133			int getNGlobalIntegrableObjects() {
134			return nGlobalIntegrableObjects_;
135			}
136	gezelter	2
137	gezelter	507	/**
138			* Returns the total number of integrable objects (total number of rigid bodies plus the total number
139			* of atoms which do not belong to the rigid bodies) in the system
140			*/
141			int getNGlobalRigidBodies() {
142			return nGlobalRigidBodies_;
143			}
144	gezelter	2
145	gezelter	507	int getNGlobalConstraints();
146			/**
147			* Returns the number of local molecules.
148			* @return the number of local molecules
149			*/
150			int getNMolecules() {
151			return molecules_.size();
152			}
153	gezelter	2
154	gezelter	507	/** Returns the number of local atoms */
155			unsigned int getNAtoms() {
156			return nAtoms_;
157			}
158	gezelter	2
159	gezelter	507	/** Returns the number of local bonds */
160			unsigned int getNBonds(){
161			return nBonds_;
162			}
163	gezelter	2
164	gezelter	507	/** Returns the number of local bends */
165			unsigned int getNBends() {
166			return nBends_;
167			}
168	gezelter	2
169	gezelter	507	/** Returns the number of local torsions */
170			unsigned int getNTorsions() {
171			return nTorsions_;
172			}
173	gezelter	2
174	gezelter	507	/** Returns the number of local rigid bodies */
175			unsigned int getNRigidBodies() {
176			return nRigidBodies_;
177			}
178	gezelter	2
179	gezelter	507	/** Returns the number of local integrable objects */
180			unsigned int getNIntegrableObjects() {
181			return nIntegrableObjects_;
182			}
183	gezelter	2
184	gezelter	507	/** Returns the number of local cutoff groups */
185			unsigned int getNCutoffGroups() {
186			return nCutoffGroups_;
187			}
188	gezelter	2
189	gezelter	507	/** Returns the total number of constraints in this SimInfo */
190			unsigned int getNConstraints() {
191			return nConstraints_;
192			}
193	gezelter	246
194	gezelter	507	/**
195			* Returns the first molecule in this SimInfo and intialize the iterator.
196			* @return the first molecule, return NULL if there is not molecule in this SimInfo
197			* @param i the iterator of molecule array (user shouldn't change it)
198			*/
199			Molecule* beginMolecule(MoleculeIterator& i);
200	gezelter	2
201	gezelter	507	/**
202			* Returns the next avaliable Molecule based on the iterator.
203			* @return the next avaliable molecule, return NULL if reaching the end of the array
204			* @param i the iterator of molecule array
205			*/
206			Molecule* nextMolecule(MoleculeIterator& i);
207	gezelter	2
208	gezelter	507	/** Returns the number of degrees of freedom */
209			int getNdf() {
210			return ndf_;
211			}
212	gezelter	2
213	gezelter	507	/** Returns the number of raw degrees of freedom */
214			int getNdfRaw() {
215			return ndfRaw_;
216			}
217	gezelter	2
218	gezelter	507	/** Returns the number of translational degrees of freedom */
219			int getNdfTrans() {
220			return ndfTrans_;
221			}
222	gezelter	2
223	gezelter	507	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
224	gezelter	246
225	gezelter	507	/** Returns the total number of z-constraint molecules in the system */
226			int getNZconstraint() {
227			return nZconstraint_;
228			}
229	gezelter	2
230	gezelter	507	/**
231			* Sets the number of z-constraint molecules in the system.
232			*/
233			void setNZconstraint(int nZconstraint) {
234			nZconstraint_ = nZconstraint;
235			}
236	gezelter	246
237	gezelter	507	/** Returns the snapshot manager. */
238			SnapshotManager* getSnapshotManager() {
239			return sman_;
240			}
241	gezelter	2
242	gezelter	507	/** Sets the snapshot manager. */
243			void setSnapshotManager(SnapshotManager* sman);
244	gezelter	246
245	gezelter	507	/** Returns the force field */
246			ForceField* getForceField() {
247			return forceField_;
248			}
249	gezelter	2
250	gezelter	507	Globals* getSimParams() {
251			return simParams_;
252			}
253	gezelter	2
254	gezelter	507	/** Returns the velocity of center of mass of the whole system.*/
255			Vector3d getComVel();
256	gezelter	2
257	gezelter	507	/** Returns the center of the mass of the whole system.*/
258			Vector3d getCom();
259	chuckv	555	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
260			void getComAll(Vector3d& com,Vector3d& comVel);
261	gezelter	2
262	chuckv	555	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
263			void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
264
265			/** Returns system angular momentum */
266			Vector3d getAngularMomentum();
267
268	gezelter	507	/** main driver function to interact with fortran during the initialization and molecule migration */
269			void update();
270	gezelter	2
271	gezelter	507	/** Returns the local index manager */
272			LocalIndexManager* getLocalIndexManager() {
273			return &localIndexMan_;
274			}
275	gezelter	2
276	gezelter	507	int getMoleculeStampId(int globalIndex) {
277			//assert(globalIndex < molStampIds_.size())
278			return molStampIds_[globalIndex];
279			}
280	gezelter	2
281	gezelter	507	/** Returns the molecule stamp */
282			MoleculeStamp* getMoleculeStamp(int id) {
283			return moleculeStamps_[id];
284			}
285	gezelter	2
286	gezelter	507	/** Return the total number of the molecule stamps */
287			int getNMoleculeStamp() {
288			return moleculeStamps_.size();
289			}
290			/**
291			* Finds a molecule with a specified global index
292			* @return a pointer point to found molecule
293			* @param index
294			*/
295			Molecule* getMoleculeByGlobalIndex(int index) {
296			MoleculeIterator i;
297			i = molecules_.find(index);
298	gezelter	2
299	gezelter	507	return i != molecules_.end() ? i->second : NULL;
300			}
301	gezelter	2
302	gezelter	507	double getRcut() {
303			return rcut_;
304			}
305	gezelter	2
306	gezelter	507	double getRsw() {
307			return rsw_;
308			}
309	gezelter	764
310			double getList() {
311			return rlist_;
312			}
313	gezelter	246
314	gezelter	507	std::string getFinalConfigFileName() {
315			return finalConfigFileName_;
316			}
317	gezelter	246
318	gezelter	507	void setFinalConfigFileName(const std::string& fileName) {
319			finalConfigFileName_ = fileName;
320			}
321	gezelter	2
322	gezelter	507	std::string getDumpFileName() {
323			return dumpFileName_;
324			}
325	gezelter	246
326	gezelter	507	void setDumpFileName(const std::string& fileName) {
327			dumpFileName_ = fileName;
328			}
329	gezelter	2
330	gezelter	507	std::string getStatFileName() {
331			return statFileName_;
332			}
333	gezelter	246
334	gezelter	507	void setStatFileName(const std::string& fileName) {
335			statFileName_ = fileName;
336			}
337	chrisfen	417
338	gezelter	507	std::string getRestFileName() {
339			return restFileName_;
340			}
341	chrisfen	417
342	gezelter	507	void setRestFileName(const std::string& fileName) {
343			restFileName_ = fileName;
344			}
345	gezelter	2
346	gezelter	507	/**
347			* Sets GlobalGroupMembership
348			* @see #SimCreator::setGlobalIndex
349			*/
350			void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
351			assert(globalGroupMembership.size() == nGlobalAtoms_);
352			globalGroupMembership_ = globalGroupMembership;
353			}
354	gezelter	2
355	gezelter	507	/**
356			* Sets GlobalMolMembership
357			* @see #SimCreator::setGlobalIndex
358			*/
359			void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
360			assert(globalMolMembership.size() == nGlobalAtoms_);
361			globalMolMembership_ = globalMolMembership;
362			}
363	gezelter	246
364
365	gezelter	507	bool isFortranInitialized() {
366			return fortranInitialized_;
367			}
368	gezelter	246
369	gezelter	507	//below functions are just forward functions
370			//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
371			//the other hand, has-a relation need composing.
372			/**
373			* Adds property into property map
374			* @param genData GenericData to be added into PropertyMap
375			*/
376			void addProperty(GenericData* genData);
377	gezelter	246
378	gezelter	507	/**
379			* Removes property from PropertyMap by name
380			* @param propName the name of property to be removed
381			*/
382			void removeProperty(const std::string& propName);
383	gezelter	246
384	gezelter	507	/**
385			* clear all of the properties
386			*/
387			void clearProperties();
388	gezelter	246
389	gezelter	507	/**
390			* Returns all names of properties
391			* @return all names of properties
392			*/
393			std::vector<std::string> getPropertyNames();
394	gezelter	246
395	gezelter	507	/**
396			* Returns all of the properties in PropertyMap
397			* @return all of the properties in PropertyMap
398			*/
399			std::vector<GenericData*> getProperties();
400	gezelter	246
401	gezelter	507	/**
402			* Returns property
403			* @param propName name of property
404			* @return a pointer point to property with propName. If no property named propName
405			* exists, return NULL
406			*/
407			GenericData* getPropertyByName(const std::string& propName);
408	gezelter	246
409	gezelter	507	/**
410			* add all exclude pairs of a molecule into exclude list.
411			*/
412			void addExcludePairs(Molecule* mol);
413	gezelter	246
414	gezelter	507	/**
415			* remove all exclude pairs which belong to a molecule from exclude list
416			*/
417	gezelter	246
418	gezelter	507	void removeExcludePairs(Molecule* mol);
419	tim	292
420
421	gezelter	507	/** Returns the unique atom types of local processor in an array */
422			std::set<AtomType*> getUniqueAtomTypes();
423	tim	292
424	gezelter	507	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
425	tim	326
426	gezelter	507	void getCutoff(double& rcut, double& rsw);
427	gezelter	246
428	gezelter	507	private:
429	gezelter	246
430	gezelter	507	/** fill up the simtype struct*/
431			void setupSimType();
432	gezelter	246
433	gezelter	507	/**
434			* Setup Fortran Simulation
435			* @see #setupFortranParallel
436			*/
437			void setupFortranSim();
438	gezelter	246
439	gezelter	507	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
440			void setupCutoff();
441	gezelter	246
442	chrisfen	598	/** Figure out which coulombic correction method to use and pass to fortran */
443	chrisfen	604	void setupElectrostaticSummationMethod( int isError );
444	chrisfen	598
445	chrisfen	726	/** Figure out which polynomial type to use for the switching function */
446			void setupSwitchingFunction();
447
448	gezelter	507	/** Calculates the number of degress of freedom in the whole system */
449			void calcNdf();
450			void calcNdfRaw();
451			void calcNdfTrans();
452	gezelter	246
453	tim	770	ForceField* forceField_;
454			Globals* simParams_;
455
456			std::map<int, Molecule> molecules_; /< Molecule array /
457
458	gezelter	507	/**
459			* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
460			* system.
461			*/
462			void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
463	gezelter	246
464	gezelter	507	//degress of freedom
465			int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
466			int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
467			int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
468			int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
469	gezelter	246
470	gezelter	507	//number of global objects
471			int nGlobalMols_; /*< number of molecules in the system /
472			int nGlobalAtoms_; /*< number of atoms in the system /
473			int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
474			int nGlobalIntegrableObjects_; /*< number of integrable objects in this system /
475			int nGlobalRigidBodies_; /*< number of rigid bodies in this system /
476			/**
477			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
478			* corresponding content is the global index of cutoff group this atom belong to.
479			* It is filled by SimCreator once and only once, since it never changed during the simulation.
480			*/
481			std::vector<int> globalGroupMembership_;
482	gezelter	246
483	gezelter	507	/**
484			* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
485			* corresponding content is the global index of molecule this atom belong to.
486			* It is filled by SimCreator once and only once, since it is never changed during the simulation.
487			*/
488			std::vector<int> globalMolMembership_;
489	gezelter	246
490
491	gezelter	507	std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
492			std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
493	gezelter	246
494	gezelter	507	//number of local objects
495			int nAtoms_; /*< number of atoms in local processor /
496			int nBonds_; /*< number of bonds in local processor /
497			int nBends_; /*< number of bends in local processor /
498			int nTorsions_; /*< number of torsions in local processor /
499			int nRigidBodies_; /*< number of rigid bodies in local processor /
500			int nIntegrableObjects_; /*< number of integrable objects in local processor /
501			int nCutoffGroups_; /*< number of cutoff groups in local processor /
502			int nConstraints_; /*< number of constraints in local processors /
503	gezelter	246
504	gezelter	507	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
505			Exclude exclude_;
506			PropertyMap properties_; /*< Generic Property /
507			SnapshotManager* sman_; /*< SnapshotManager /
508	gezelter	246
509	gezelter	507	/**
510			* The reason to have a local index manager is that when molecule is migrating to other processors,
511			* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
512			* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
513			* to make a efficient data moving plan.
514			*/
515			LocalIndexManager localIndexMan_;
516	gezelter	246
517	gezelter	507	//file names
518			std::string finalConfigFileName_;
519			std::string dumpFileName_;
520			std::string statFileName_;
521			std::string restFileName_;
522	chrisfen	417
523	gezelter	507	double rcut_; /*< cutoff radius/
524			double rsw_; /*< radius of switching function/
525	gezelter	764	double rlist_; /*< neighbor list radius /
526	gezelter	246
527	gezelter	507	bool fortranInitialized_; /*< flag indicate whether fortran side is initialized /
528	tim	292
529	gezelter	246	#ifdef IS_MPI
530			//in Parallel version, we need MolToProc
531	gezelter	507	public:
532	gezelter	246
533	gezelter	507	/**
534			* Finds the processor where a molecule resides
535			* @return the id of the processor which contains the molecule
536			* @param globalIndex global Index of the molecule
537			*/
538			int getMolToProc(int globalIndex) {
539			//assert(globalIndex < molToProcMap_.size());
540			return molToProcMap_[globalIndex];
541			}
542	gezelter	246
543	gezelter	507	/**
544			* Set MolToProcMap array
545			* @see #SimCreator::divideMolecules
546			*/
547			void setMolToProcMap(const std::vector<int>& molToProcMap) {
548			molToProcMap_ = molToProcMap;
549			}
550	gezelter	246
551	gezelter	507	private:
552	gezelter	246
553	gezelter	507	void setupFortranParallel();
554	gezelter	246
555	gezelter	507	/**
556			* The size of molToProcMap_ is equal to total number of molecules in the system.
557			* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
558			* once.
559			*/
560			std::vector<int> molToProcMap_;
561	tim	292
562	gezelter	246	#endif
563
564	gezelter	507	};
565	gezelter	2
566	gezelter	246	} //namespace oopse
567			#endif //BRAINS_SIMMODEL_HPP
568	gezelter	2