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 StuntDouble;
  /**
   * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" 
   * @brief One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules.
    * The Molecule class maintains all of the concrete objects 
    * (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups, 
    * constraints). In both the single and parallel versions, atoms and
    * rigid bodies have both global and local indices.  The local index is 
    * not relevant to molecules or cutoff groups.
    */
  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 torsions */        
    unsigned int getNInversions() {
      return nInversions_;
    }
    /** 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_ - getFdf();
    }

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

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

    /** sets the current number of frozen degrees of freedom */
    void setFdf(int fdf) {
      fdf_local = fdf;
    }

    int getFdf(); 
    
    //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();

    /** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
    void getGyrationalVolume(RealType &vol);
    /** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
    void getGyrationalVolume(RealType &vol, RealType &detI);
    /** 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;
    }

    RealType getRcut() {
      return rcut_;
    }

    RealType getRsw() {
      return rsw_;
    }

    RealType getList() {
      return rlist_;
    }
        
    std::string getFinalConfigFileName() {
      return finalConfigFileName_;
    }

    void setFinalConfigFileName(const std::string& fileName) {
      finalConfigFileName_ = fileName;
    }

    std::string getRawMetaData() {
      return rawMetaData_;
    }
    void setRawMetaData(const std::string& rawMetaData) {
      rawMetaData_ = rawMetaData;
    }
        
    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_;
    }
        
    bool getCalcBoxDipole() {
      return calcBoxDipole_;
    }

    bool getUseAtomicVirial() {
      return useAtomicVirial_;
    }

    //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(RealType& rcut, RealType& 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();

    /** Determine if we need to accumulate the simulation box dipole */
    void setupAccumulateBoxDipole();

    /** 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 fdf_local;       /**< number of frozen degrees of freedom */
    int fdf_;            /**< number of frozen degrees of freedom */
    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 nInversions_;         /**< number of inversions 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_;

    // unparsed MetaData block for storing in Dump and EOR files:
    std::string rawMetaData_;

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

    bool ljsp_; /**< use shifted potential for LJ*/
    bool ljsf_; /**< use shifted force for LJ*/

    bool fortranInitialized_; /**< flag indicate whether fortran side 
                                 is initialized */
    
    bool calcBoxDipole_; /**< flag to indicate whether or not we calculate 
                            the simulation box dipole moment */
    
    bool useAtomicVirial_; /**< flag to indicate whether or not we use 
                              Atomic Virials to calculate the pressure */

    public:
     /**
      * return an integral objects by its global index. In MPI version, if the StuntDouble with specified
      * global index does not belong to local processor, a NULL will be return.
      */
      StuntDouble* getIOIndexToIntegrableObject(int index);
      void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
    private:
      std::vector<StuntDouble*> IOIndexToIntegrableObject;
  //public:
    //void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
    /**
     * return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
     * global index does not belong to local processor, a NULL will be return.
     */
    //StuntDouble* getStuntDoubleFromGlobalIndex(int index);
  //private:
    //std::vector<StuntDouble*> sdByGlobalIndex_;
    
    //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_; 


  };

} //namespace oopse
#endif //BRAINS_SIMMODEL_HPP

Revision:	1277
Committed:	Mon Jul 14 12:35:58 2008 UTC (16 years, 9 months ago) by gezelter
Original Path:	*trunk/src/brains/SimInfo.hpp*
File size:	21015 byte(s)
Log Message:	Changes for implementing Amber force field: Added Inversions and worked on BaseAtomTypes so that they'd function with the fortran side.
#	Content
1	/*
2	* 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
49	#ifndef BRAINS_SIMMODEL_HPP
50	#define BRAINS_SIMMODEL_HPP
51
52	#include <iostream>
53	#include <set>
54	#include <utility>
55	#include <vector>
56
57	#include "brains/Exclude.hpp"
58	#include "io/Globals.hpp"
59	#include "math/Vector3.hpp"
60	#include "math/SquareMatrix3.hpp"
61	#include "types/MoleculeStamp.hpp"
62	#include "UseTheForce/ForceField.hpp"
63	#include "utils/PropertyMap.hpp"
64	#include "utils/LocalIndexManager.hpp"
65
66	//another nonsense macro declaration
67	#define __C
68	#include "brains/fSimulation.h"
69
70	namespace oopse{
71
72	//forward decalration
73	class SnapshotManager;
74	class Molecule;
75	class SelectionManager;
76	class StuntDouble;
77	/**
78	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
79	* @brief One of the heavy weight classes of OOPSE, SimInfo maintains a list of molecules.
80	* The Molecule class maintains all of the concrete objects
81	* (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups,
82	* constraints). In both the single and parallel versions, atoms and
83	* rigid bodies have both global and local indices. The local index is
84	* not relevant to molecules or cutoff groups.
85	*/
86	class SimInfo {
87	public:
88	typedef std::map<int, Molecule*>::iterator MoleculeIterator;
89
90	/**
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	SimInfo(ForceField* ff, Globals* simParams);
99	virtual ~SimInfo();
100
101	/**
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
108	/**
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
114	/** Returns the total number of molecules in the system. */
115	int getNGlobalMolecules() {
116	return nGlobalMols_;
117	}
118
119	/** Returns the total number of atoms in the system. */
120	int getNGlobalAtoms() {
121	return nGlobalAtoms_;
122	}
123
124	/** Returns the total number of cutoff groups in the system. */
125	int getNGlobalCutoffGroups() {
126	return nGlobalCutoffGroups_;
127	}
128
129	/**
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
137	/**
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
145	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
154	/** Returns the number of local atoms */
155	unsigned int getNAtoms() {
156	return nAtoms_;
157	}
158
159	/** Returns the number of local bonds */
160	unsigned int getNBonds(){
161	return nBonds_;
162	}
163
164	/** Returns the number of local bends */
165	unsigned int getNBends() {
166	return nBends_;
167	}
168
169	/** Returns the number of local torsions */
170	unsigned int getNTorsions() {
171	return nTorsions_;
172	}
173
174	/** Returns the number of local torsions */
175	unsigned int getNInversions() {
176	return nInversions_;
177	}
178	/** Returns the number of local rigid bodies */
179	unsigned int getNRigidBodies() {
180	return nRigidBodies_;
181	}
182
183	/** Returns the number of local integrable objects */
184	unsigned int getNIntegrableObjects() {
185	return nIntegrableObjects_;
186	}
187
188	/** Returns the number of local cutoff groups */
189	unsigned int getNCutoffGroups() {
190	return nCutoffGroups_;
191	}
192
193	/** Returns the total number of constraints in this SimInfo */
194	unsigned int getNConstraints() {
195	return nConstraints_;
196	}
197
198	/**
199	* Returns the first molecule in this SimInfo and intialize the iterator.
200	* @return the first molecule, return NULL if there is not molecule in this SimInfo
201	* @param i the iterator of molecule array (user shouldn't change it)
202	*/
203	Molecule* beginMolecule(MoleculeIterator& i);
204
205	/**
206	* Returns the next avaliable Molecule based on the iterator.
207	* @return the next avaliable molecule, return NULL if reaching the end of the array
208	* @param i the iterator of molecule array
209	*/
210	Molecule* nextMolecule(MoleculeIterator& i);
211
212	/** Returns the number of degrees of freedom */
213	int getNdf() {
214	return ndf_ - getFdf();
215	}
216
217	/** Returns the number of raw degrees of freedom */
218	int getNdfRaw() {
219	return ndfRaw_;
220	}
221
222	/** Returns the number of translational degrees of freedom */
223	int getNdfTrans() {
224	return ndfTrans_;
225	}
226
227	/** sets the current number of frozen degrees of freedom */
228	void setFdf(int fdf) {
229	fdf_local = fdf;
230	}
231
232	int getFdf();
233
234	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
235
236	/** Returns the total number of z-constraint molecules in the system */
237	int getNZconstraint() {
238	return nZconstraint_;
239	}
240
241	/**
242	* Sets the number of z-constraint molecules in the system.
243	*/
244	void setNZconstraint(int nZconstraint) {
245	nZconstraint_ = nZconstraint;
246	}
247
248	/** Returns the snapshot manager. */
249	SnapshotManager* getSnapshotManager() {
250	return sman_;
251	}
252
253	/** Sets the snapshot manager. */
254	void setSnapshotManager(SnapshotManager* sman);
255
256	/** Returns the force field */
257	ForceField* getForceField() {
258	return forceField_;
259	}
260
261	Globals* getSimParams() {
262	return simParams_;
263	}
264
265	/** Returns the velocity of center of mass of the whole system.*/
266	Vector3d getComVel();
267
268	/** Returns the center of the mass of the whole system.*/
269	Vector3d getCom();
270	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
271	void getComAll(Vector3d& com,Vector3d& comVel);
272
273	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
274	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
275
276	/** Returns system angular momentum */
277	Vector3d getAngularMomentum();
278
279	/** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
280	void getGyrationalVolume(RealType &vol);
281	/** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
282	void getGyrationalVolume(RealType &vol, RealType &detI);
283	/** main driver function to interact with fortran during the initialization and molecule migration */
284	void update();
285
286	/** Returns the local index manager */
287	LocalIndexManager* getLocalIndexManager() {
288	return &localIndexMan_;
289	}
290
291	int getMoleculeStampId(int globalIndex) {
292	//assert(globalIndex < molStampIds_.size())
293	return molStampIds_[globalIndex];
294	}
295
296	/** Returns the molecule stamp */
297	MoleculeStamp* getMoleculeStamp(int id) {
298	return moleculeStamps_[id];
299	}
300
301	/** Return the total number of the molecule stamps */
302	int getNMoleculeStamp() {
303	return moleculeStamps_.size();
304	}
305	/**
306	* Finds a molecule with a specified global index
307	* @return a pointer point to found molecule
308	* @param index
309	*/
310	Molecule* getMoleculeByGlobalIndex(int index) {
311	MoleculeIterator i;
312	i = molecules_.find(index);
313
314	return i != molecules_.end() ? i->second : NULL;
315	}
316
317	RealType getRcut() {
318	return rcut_;
319	}
320
321	RealType getRsw() {
322	return rsw_;
323	}
324
325	RealType getList() {
326	return rlist_;
327	}
328
329	std::string getFinalConfigFileName() {
330	return finalConfigFileName_;
331	}
332
333	void setFinalConfigFileName(const std::string& fileName) {
334	finalConfigFileName_ = fileName;
335	}
336
337	std::string getRawMetaData() {
338	return rawMetaData_;
339	}
340	void setRawMetaData(const std::string& rawMetaData) {
341	rawMetaData_ = rawMetaData;
342	}
343
344	std::string getDumpFileName() {
345	return dumpFileName_;
346	}
347
348	void setDumpFileName(const std::string& fileName) {
349	dumpFileName_ = fileName;
350	}
351
352	std::string getStatFileName() {
353	return statFileName_;
354	}
355
356	void setStatFileName(const std::string& fileName) {
357	statFileName_ = fileName;
358	}
359
360	std::string getRestFileName() {
361	return restFileName_;
362	}
363
364	void setRestFileName(const std::string& fileName) {
365	restFileName_ = fileName;
366	}
367
368	/**
369	* Sets GlobalGroupMembership
370	* @see #SimCreator::setGlobalIndex
371	*/
372	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
373	assert(globalGroupMembership.size() == nGlobalAtoms_);
374	globalGroupMembership_ = globalGroupMembership;
375	}
376
377	/**
378	* Sets GlobalMolMembership
379	* @see #SimCreator::setGlobalIndex
380	*/
381	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
382	assert(globalMolMembership.size() == nGlobalAtoms_);
383	globalMolMembership_ = globalMolMembership;
384	}
385
386
387	bool isFortranInitialized() {
388	return fortranInitialized_;
389	}
390
391	bool getCalcBoxDipole() {
392	return calcBoxDipole_;
393	}
394
395	bool getUseAtomicVirial() {
396	return useAtomicVirial_;
397	}
398
399	//below functions are just forward functions
400	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
401	//the other hand, has-a relation need composing.
402	/**
403	* Adds property into property map
404	* @param genData GenericData to be added into PropertyMap
405	*/
406	void addProperty(GenericData* genData);
407
408	/**
409	* Removes property from PropertyMap by name
410	* @param propName the name of property to be removed
411	*/
412	void removeProperty(const std::string& propName);
413
414	/**
415	* clear all of the properties
416	*/
417	void clearProperties();
418
419	/**
420	* Returns all names of properties
421	* @return all names of properties
422	*/
423	std::vector<std::string> getPropertyNames();
424
425	/**
426	* Returns all of the properties in PropertyMap
427	* @return all of the properties in PropertyMap
428	*/
429	std::vector<GenericData*> getProperties();
430
431	/**
432	* Returns property
433	* @param propName name of property
434	* @return a pointer point to property with propName. If no property named propName
435	* exists, return NULL
436	*/
437	GenericData* getPropertyByName(const std::string& propName);
438
439	/**
440	* add all exclude pairs of a molecule into exclude list.
441	*/
442	void addExcludePairs(Molecule* mol);
443
444	/**
445	* remove all exclude pairs which belong to a molecule from exclude list
446	*/
447
448	void removeExcludePairs(Molecule* mol);
449
450
451	/** Returns the unique atom types of local processor in an array */
452	std::set<AtomType*> getUniqueAtomTypes();
453
454	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
455
456	void getCutoff(RealType& rcut, RealType& rsw);
457
458	private:
459
460	/** fill up the simtype struct*/
461	void setupSimType();
462
463	/**
464	* Setup Fortran Simulation
465	* @see #setupFortranParallel
466	*/
467	void setupFortranSim();
468
469	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
470	void setupCutoff();
471
472	/** Figure out which coulombic correction method to use and pass to fortran */
473	void setupElectrostaticSummationMethod( int isError );
474
475	/** Figure out which polynomial type to use for the switching function */
476	void setupSwitchingFunction();
477
478	/** Determine if we need to accumulate the simulation box dipole */
479	void setupAccumulateBoxDipole();
480
481	/** Calculates the number of degress of freedom in the whole system */
482	void calcNdf();
483	void calcNdfRaw();
484	void calcNdfTrans();
485
486	ForceField* forceField_;
487	Globals* simParams_;
488
489	std::map<int, Molecule> molecules_; /< Molecule array /
490
491	/**
492	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
493	* system.
494	*/
495	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
496
497	//degress of freedom
498	int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
499	int fdf_local; /*< number of frozen degrees of freedom /
500	int fdf_; /*< number of frozen degrees of freedom /
501	int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
502	int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
503	int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
504
505	//number of global objects
506	int nGlobalMols_; /*< number of molecules in the system /
507	int nGlobalAtoms_; /*< number of atoms in the system /
508	int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
509	int nGlobalIntegrableObjects_; /*< number of integrable objects in this system /
510	int nGlobalRigidBodies_; /*< number of rigid bodies in this system /
511	/**
512	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
513	* corresponding content is the global index of cutoff group this atom belong to.
514	* It is filled by SimCreator once and only once, since it never changed during the simulation.
515	*/
516	std::vector<int> globalGroupMembership_;
517
518	/**
519	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
520	* corresponding content is the global index of molecule this atom belong to.
521	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
522	*/
523	std::vector<int> globalMolMembership_;
524
525
526	std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
527	std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
528
529	//number of local objects
530	int nAtoms_; /*< number of atoms in local processor /
531	int nBonds_; /*< number of bonds in local processor /
532	int nBends_; /*< number of bends in local processor /
533	int nTorsions_; /*< number of torsions in local processor /
534	int nInversions_; /*< number of inversions in local processor /
535	int nRigidBodies_; /*< number of rigid bodies in local processor /
536	int nIntegrableObjects_; /*< number of integrable objects in local processor /
537	int nCutoffGroups_; /*< number of cutoff groups in local processor /
538	int nConstraints_; /*< number of constraints in local processors /
539
540	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
541	Exclude exclude_;
542	PropertyMap properties_; /*< Generic Property /
543	SnapshotManager* sman_; /*< SnapshotManager /
544
545	/**
546	* The reason to have a local index manager is that when molecule is migrating to other processors,
547	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
548	* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
549	* to make a efficient data moving plan.
550	*/
551	LocalIndexManager localIndexMan_;
552
553	// unparsed MetaData block for storing in Dump and EOR files:
554	std::string rawMetaData_;
555
556	//file names
557	std::string finalConfigFileName_;
558	std::string dumpFileName_;
559	std::string statFileName_;
560	std::string restFileName_;
561
562	RealType rcut_; /*< cutoff radius/
563	RealType rsw_; /*< radius of switching function/
564	RealType rlist_; /*< neighbor list radius /
565
566	bool ljsp_; /*< use shifted potential for LJ/
567	bool ljsf_; /*< use shifted force for LJ/
568
569	bool fortranInitialized_; /**< flag indicate whether fortran side
570	is initialized */
571
572	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
573	the simulation box dipole moment */
574
575	bool useAtomicVirial_; /**< flag to indicate whether or not we use
576	Atomic Virials to calculate the pressure */
577
578	public:
579	/**
580	* return an integral objects by its global index. In MPI version, if the StuntDouble with specified
581	* global index does not belong to local processor, a NULL will be return.
582	*/
583	StuntDouble* getIOIndexToIntegrableObject(int index);
584	void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
585	private:
586	std::vector<StuntDouble*> IOIndexToIntegrableObject;
587	//public:
588	//void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
589	/**
590	* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
591	* global index does not belong to local processor, a NULL will be return.
592	*/
593	//StuntDouble* getStuntDoubleFromGlobalIndex(int index);
594	//private:
595	//std::vector<StuntDouble*> sdByGlobalIndex_;
596
597	//in Parallel version, we need MolToProc
598	public:
599
600	/**
601	* Finds the processor where a molecule resides
602	* @return the id of the processor which contains the molecule
603	* @param globalIndex global Index of the molecule
604	*/
605	int getMolToProc(int globalIndex) {
606	//assert(globalIndex < molToProcMap_.size());
607	return molToProcMap_[globalIndex];
608	}
609
610	/**
611	* Set MolToProcMap array
612	* @see #SimCreator::divideMolecules
613	*/
614	void setMolToProcMap(const std::vector<int>& molToProcMap) {
615	molToProcMap_ = molToProcMap;
616	}
617
618	private:
619
620	void setupFortranParallel();
621
622	/**
623	* The size of molToProcMap_ is equal to total number of molecules
624	* in the system. It maps a molecule to the processor on which it
625	* resides. it is filled by SimCreator once and only once.
626	*/
627	std::vector<int> molToProcMap_;
628
629
630	};
631
632	} //namespace oopse
633	#endif //BRAINS_SIMMODEL_HPP
634