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, rigid bodies, cutoff groups, constrains).
   * 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 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 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_;
    
#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:	1129
Committed:	Fri Apr 20 18:15:48 2007 UTC (18 years, 6 months ago) by chrisfen
File size:	20880 byte(s)
Log Message:	SF Lennard-Jones was added for everyones' enjoyment. The behavior is tethered to the electrostaticSummationMethod keyword.
#	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, rigid bodies, cutoff groups, constrains).
82	* 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 rigid bodies */
175	unsigned int getNRigidBodies() {
176	return nRigidBodies_;
177	}
178
179	/** Returns the number of local integrable objects */
180	unsigned int getNIntegrableObjects() {
181	return nIntegrableObjects_;
182	}
183
184	/** Returns the number of local cutoff groups */
185	unsigned int getNCutoffGroups() {
186	return nCutoffGroups_;
187	}
188
189	/** Returns the total number of constraints in this SimInfo */
190	unsigned int getNConstraints() {
191	return nConstraints_;
192	}
193
194	/**
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
201	/**
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
208	/** Returns the number of degrees of freedom */
209	int getNdf() {
210	return ndf_ - getFdf();
211	}
212
213	/** Returns the number of raw degrees of freedom */
214	int getNdfRaw() {
215	return ndfRaw_;
216	}
217
218	/** Returns the number of translational degrees of freedom */
219	int getNdfTrans() {
220	return ndfTrans_;
221	}
222
223	/** sets the current number of frozen degrees of freedom */
224	void setFdf(int fdf) {
225	fdf_local = fdf;
226	}
227
228	int getFdf();
229
230	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
231
232	/** Returns the total number of z-constraint molecules in the system */
233	int getNZconstraint() {
234	return nZconstraint_;
235	}
236
237	/**
238	* Sets the number of z-constraint molecules in the system.
239	*/
240	void setNZconstraint(int nZconstraint) {
241	nZconstraint_ = nZconstraint;
242	}
243
244	/** Returns the snapshot manager. */
245	SnapshotManager* getSnapshotManager() {
246	return sman_;
247	}
248
249	/** Sets the snapshot manager. */
250	void setSnapshotManager(SnapshotManager* sman);
251
252	/** Returns the force field */
253	ForceField* getForceField() {
254	return forceField_;
255	}
256
257	Globals* getSimParams() {
258	return simParams_;
259	}
260
261	/** Returns the velocity of center of mass of the whole system.*/
262	Vector3d getComVel();
263
264	/** Returns the center of the mass of the whole system.*/
265	Vector3d getCom();
266	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
267	void getComAll(Vector3d& com,Vector3d& comVel);
268
269	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
270	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
271
272	/** Returns system angular momentum */
273	Vector3d getAngularMomentum();
274
275	/** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
276	void getGyrationalVolume(RealType &vol);
277	/** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
278	void getGyrationalVolume(RealType &vol, RealType &detI);
279	/** main driver function to interact with fortran during the initialization and molecule migration */
280	void update();
281
282	/** Returns the local index manager */
283	LocalIndexManager* getLocalIndexManager() {
284	return &localIndexMan_;
285	}
286
287	int getMoleculeStampId(int globalIndex) {
288	//assert(globalIndex < molStampIds_.size())
289	return molStampIds_[globalIndex];
290	}
291
292	/** Returns the molecule stamp */
293	MoleculeStamp* getMoleculeStamp(int id) {
294	return moleculeStamps_[id];
295	}
296
297	/** Return the total number of the molecule stamps */
298	int getNMoleculeStamp() {
299	return moleculeStamps_.size();
300	}
301	/**
302	* Finds a molecule with a specified global index
303	* @return a pointer point to found molecule
304	* @param index
305	*/
306	Molecule* getMoleculeByGlobalIndex(int index) {
307	MoleculeIterator i;
308	i = molecules_.find(index);
309
310	return i != molecules_.end() ? i->second : NULL;
311	}
312
313	RealType getRcut() {
314	return rcut_;
315	}
316
317	RealType getRsw() {
318	return rsw_;
319	}
320
321	RealType getList() {
322	return rlist_;
323	}
324
325	std::string getFinalConfigFileName() {
326	return finalConfigFileName_;
327	}
328
329	void setFinalConfigFileName(const std::string& fileName) {
330	finalConfigFileName_ = fileName;
331	}
332
333	std::string getRawMetaData() {
334	return rawMetaData_;
335	}
336	void setRawMetaData(const std::string& rawMetaData) {
337	rawMetaData_ = rawMetaData;
338	}
339
340	std::string getDumpFileName() {
341	return dumpFileName_;
342	}
343
344	void setDumpFileName(const std::string& fileName) {
345	dumpFileName_ = fileName;
346	}
347
348	std::string getStatFileName() {
349	return statFileName_;
350	}
351
352	void setStatFileName(const std::string& fileName) {
353	statFileName_ = fileName;
354	}
355
356	std::string getRestFileName() {
357	return restFileName_;
358	}
359
360	void setRestFileName(const std::string& fileName) {
361	restFileName_ = fileName;
362	}
363
364	/**
365	* Sets GlobalGroupMembership
366	* @see #SimCreator::setGlobalIndex
367	*/
368	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
369	assert(globalGroupMembership.size() == nGlobalAtoms_);
370	globalGroupMembership_ = globalGroupMembership;
371	}
372
373	/**
374	* Sets GlobalMolMembership
375	* @see #SimCreator::setGlobalIndex
376	*/
377	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
378	assert(globalMolMembership.size() == nGlobalAtoms_);
379	globalMolMembership_ = globalMolMembership;
380	}
381
382
383	bool isFortranInitialized() {
384	return fortranInitialized_;
385	}
386
387	bool getCalcBoxDipole() {
388	return calcBoxDipole_;
389	}
390
391	bool getUseAtomicVirial() {
392	return useAtomicVirial_;
393	}
394
395	//below functions are just forward functions
396	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
397	//the other hand, has-a relation need composing.
398	/**
399	* Adds property into property map
400	* @param genData GenericData to be added into PropertyMap
401	*/
402	void addProperty(GenericData* genData);
403
404	/**
405	* Removes property from PropertyMap by name
406	* @param propName the name of property to be removed
407	*/
408	void removeProperty(const std::string& propName);
409
410	/**
411	* clear all of the properties
412	*/
413	void clearProperties();
414
415	/**
416	* Returns all names of properties
417	* @return all names of properties
418	*/
419	std::vector<std::string> getPropertyNames();
420
421	/**
422	* Returns all of the properties in PropertyMap
423	* @return all of the properties in PropertyMap
424	*/
425	std::vector<GenericData*> getProperties();
426
427	/**
428	* Returns property
429	* @param propName name of property
430	* @return a pointer point to property with propName. If no property named propName
431	* exists, return NULL
432	*/
433	GenericData* getPropertyByName(const std::string& propName);
434
435	/**
436	* add all exclude pairs of a molecule into exclude list.
437	*/
438	void addExcludePairs(Molecule* mol);
439
440	/**
441	* remove all exclude pairs which belong to a molecule from exclude list
442	*/
443
444	void removeExcludePairs(Molecule* mol);
445
446
447	/** Returns the unique atom types of local processor in an array */
448	std::set<AtomType*> getUniqueAtomTypes();
449
450	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
451
452	void getCutoff(RealType& rcut, RealType& rsw);
453
454	private:
455
456	/** fill up the simtype struct*/
457	void setupSimType();
458
459	/**
460	* Setup Fortran Simulation
461	* @see #setupFortranParallel
462	*/
463	void setupFortranSim();
464
465	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
466	void setupCutoff();
467
468	/** Figure out which coulombic correction method to use and pass to fortran */
469	void setupElectrostaticSummationMethod( int isError );
470
471	/** Figure out which polynomial type to use for the switching function */
472	void setupSwitchingFunction();
473
474	/** Determine if we need to accumulate the simulation box dipole */
475	void setupAccumulateBoxDipole();
476
477	/** Calculates the number of degress of freedom in the whole system */
478	void calcNdf();
479	void calcNdfRaw();
480	void calcNdfTrans();
481
482	ForceField* forceField_;
483	Globals* simParams_;
484
485	std::map<int, Molecule> molecules_; /< Molecule array /
486
487	/**
488	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
489	* system.
490	*/
491	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
492
493	//degress of freedom
494	int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
495	int fdf_local; /*< number of frozen degrees of freedom /
496	int fdf_; /*< number of frozen degrees of freedom /
497	int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
498	int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
499	int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
500
501	//number of global objects
502	int nGlobalMols_; /*< number of molecules in the system /
503	int nGlobalAtoms_; /*< number of atoms in the system /
504	int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
505	int nGlobalIntegrableObjects_; /*< number of integrable objects in this system /
506	int nGlobalRigidBodies_; /*< number of rigid bodies in this system /
507	/**
508	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
509	* corresponding content is the global index of cutoff group this atom belong to.
510	* It is filled by SimCreator once and only once, since it never changed during the simulation.
511	*/
512	std::vector<int> globalGroupMembership_;
513
514	/**
515	* the size of globalGroupMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
516	* corresponding content is the global index of molecule this atom belong to.
517	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
518	*/
519	std::vector<int> globalMolMembership_;
520
521
522	std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
523	std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
524
525	//number of local objects
526	int nAtoms_; /*< number of atoms in local processor /
527	int nBonds_; /*< number of bonds in local processor /
528	int nBends_; /*< number of bends in local processor /
529	int nTorsions_; /*< number of torsions in local processor /
530	int nRigidBodies_; /*< number of rigid bodies in local processor /
531	int nIntegrableObjects_; /*< number of integrable objects in local processor /
532	int nCutoffGroups_; /*< number of cutoff groups in local processor /
533	int nConstraints_; /*< number of constraints in local processors /
534
535	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
536	Exclude exclude_;
537	PropertyMap properties_; /*< Generic Property /
538	SnapshotManager* sman_; /*< SnapshotManager /
539
540	/**
541	* The reason to have a local index manager is that when molecule is migrating to other processors,
542	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
543	* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
544	* to make a efficient data moving plan.
545	*/
546	LocalIndexManager localIndexMan_;
547
548	// unparsed MetaData block for storing in Dump and EOR files:
549	std::string rawMetaData_;
550
551	//file names
552	std::string finalConfigFileName_;
553	std::string dumpFileName_;
554	std::string statFileName_;
555	std::string restFileName_;
556
557	RealType rcut_; /*< cutoff radius/
558	RealType rsw_; /*< radius of switching function/
559	RealType rlist_; /*< neighbor list radius /
560
561	bool ljsp_; /*< use shifted potential for LJ/
562	bool ljsf_; /*< use shifted force for LJ/
563
564	bool fortranInitialized_; /**< flag indicate whether fortran side
565	is initialized */
566
567	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
568	the simulation box dipole moment */
569
570	bool useAtomicVirial_; /**< flag to indicate whether or not we use
571	Atomic Virials to calculate the pressure */
572
573	public:
574	/**
575	* return an integral objects by its global index. In MPI version, if the StuntDouble with specified
576	* global index does not belong to local processor, a NULL will be return.
577	*/
578	StuntDouble* getIOIndexToIntegrableObject(int index);
579	void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
580	private:
581	std::vector<StuntDouble*> IOIndexToIntegrableObject;
582	//public:
583	//void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
584	/**
585	* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
586	* global index does not belong to local processor, a NULL will be return.
587	*/
588	//StuntDouble* getStuntDoubleFromGlobalIndex(int index);
589	//private:
590	//std::vector<StuntDouble*> sdByGlobalIndex_;
591
592	#ifdef IS_MPI
593	//in Parallel version, we need MolToProc
594	public:
595
596	/**
597	* Finds the processor where a molecule resides
598	* @return the id of the processor which contains the molecule
599	* @param globalIndex global Index of the molecule
600	*/
601	int getMolToProc(int globalIndex) {
602	//assert(globalIndex < molToProcMap_.size());
603	return molToProcMap_[globalIndex];
604	}
605
606	/**
607	* Set MolToProcMap array
608	* @see #SimCreator::divideMolecules
609	*/
610	void setMolToProcMap(const std::vector<int>& molToProcMap) {
611	molToProcMap_ = molToProcMap;
612	}
613
614
615
616	private:
617
618	void setupFortranParallel();
619
620	/**
621	* The size of molToProcMap_ is equal to total number of molecules in the system.
622	* It maps a molecule to the processor on which it resides. it is filled by SimCreator once and only
623	* once.
624	*/
625	std::vector<int> molToProcMap_;
626
627	#endif
628
629	};
630
631	} //namespace oopse
632	#endif //BRAINS_SIMMODEL_HPP
633