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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Vardeman & Gezelter, in progress (2009).                        
 */
 
/**
 * @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/PairList.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"
#include "nonbonded/Electrostatic.hpp"

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

namespace OpenMD{

  //forward decalration 
  class SnapshotManager;
  class Molecule;
  class SelectionManager;
  class StuntDouble;
  class Electrostatic;
  /**
   * @class SimInfo SimInfo.hpp "brains/SimInfo.hpp" 
   * @brief One of the heavy weight classes of OpenMD, 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;
    }

    int getGlobalMolMembership(int id){
      return globalMolMembership_[id];
    }

    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() == static_cast<size_t>(nGlobalAtoms_));
      globalGroupMembership_ = globalGroupMembership;
    }

    /** 
     * Sets GlobalMolMembership
     * @see #SimCreator::setGlobalIndex
     */        
    void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
      assert(globalMolMembership.size() == static_cast<size_t>(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 special interaction pairs (including excluded
     * interactions) in a molecule into the appropriate lists.
     */
    void addInteractionPairs(Molecule* mol);

    /**
     * remove all special interaction pairs which belong to a molecule
     * from the appropriate lists.
     */
    void removeInteractionPairs(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 globalMolMembership_  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*/
    PairList excludedInteractions_;      
    PairList oneTwoInteractions_;      
    PairList oneThreeInteractions_;      
    PairList oneFourInteractions_;      
    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 */

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

    bool fortranInitialized_; /** flag to indicate whether the 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 OpenMD
#endif //BRAINS_SIMMODEL_HPP

Revision:	1503
Committed:	Sat Oct 2 19:54:41 2010 UTC (14 years, 7 months ago) by gezelter
File size:	21460 byte(s)
Log Message:	Changes to remove more of the low level stuff from 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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Vardeman & Gezelter, in progress (2009).
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/PairList.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	#include "nonbonded/Electrostatic.hpp"
66
67	//another nonsense macro declaration
68	#define __OPENMD_C
69	#include "brains/fSimulation.h"
70
71	namespace OpenMD{
72
73	//forward decalration
74	class SnapshotManager;
75	class Molecule;
76	class SelectionManager;
77	class StuntDouble;
78	class Electrostatic;
79	/**
80	* @class SimInfo SimInfo.hpp "brains/SimInfo.hpp"
81	* @brief One of the heavy weight classes of OpenMD, SimInfo maintains a list of molecules.
82	* The Molecule class maintains all of the concrete objects
83	* (atoms, bond, bend, torsions, inversions, rigid bodies, cutoff groups,
84	* constraints). In both the single and parallel versions, atoms and
85	* rigid bodies have both global and local indices. The local index is
86	* not relevant to molecules or cutoff groups.
87	*/
88	class SimInfo {
89	public:
90	typedef std::map<int, Molecule*>::iterator MoleculeIterator;
91
92	/**
93	* Constructor of SimInfo
94	* @param molStampPairs MoleculeStamp Array. The first element of the pair is molecule stamp, the
95	* second element is the total number of molecules with the same molecule stamp in the system
96	* @param ff pointer of a concrete ForceField instance
97	* @param simParams
98	* @note
99	*/
100	SimInfo(ForceField* ff, Globals* simParams);
101	virtual ~SimInfo();
102
103	/**
104	* Adds a molecule
105	* @return return true if adding successfully, return false if the molecule is already in SimInfo
106	* @param mol molecule to be added
107	*/
108	bool addMolecule(Molecule* mol);
109
110	/**
111	* Removes a molecule from SimInfo
112	* @return true if removing successfully, return false if molecule is not in this SimInfo
113	*/
114	bool removeMolecule(Molecule* mol);
115
116	/** Returns the total number of molecules in the system. */
117	int getNGlobalMolecules() {
118	return nGlobalMols_;
119	}
120
121	/** Returns the total number of atoms in the system. */
122	int getNGlobalAtoms() {
123	return nGlobalAtoms_;
124	}
125
126	/** Returns the total number of cutoff groups in the system. */
127	int getNGlobalCutoffGroups() {
128	return nGlobalCutoffGroups_;
129	}
130
131	/**
132	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
133	* of atoms which do not belong to the rigid bodies) in the system
134	*/
135	int getNGlobalIntegrableObjects() {
136	return nGlobalIntegrableObjects_;
137	}
138
139	/**
140	* Returns the total number of integrable objects (total number of rigid bodies plus the total number
141	* of atoms which do not belong to the rigid bodies) in the system
142	*/
143	int getNGlobalRigidBodies() {
144	return nGlobalRigidBodies_;
145	}
146
147	int getNGlobalConstraints();
148	/**
149	* Returns the number of local molecules.
150	* @return the number of local molecules
151	*/
152	int getNMolecules() {
153	return molecules_.size();
154	}
155
156	/** Returns the number of local atoms */
157	unsigned int getNAtoms() {
158	return nAtoms_;
159	}
160
161	/** Returns the number of local bonds */
162	unsigned int getNBonds(){
163	return nBonds_;
164	}
165
166	/** Returns the number of local bends */
167	unsigned int getNBends() {
168	return nBends_;
169	}
170
171	/** Returns the number of local torsions */
172	unsigned int getNTorsions() {
173	return nTorsions_;
174	}
175
176	/** Returns the number of local torsions */
177	unsigned int getNInversions() {
178	return nInversions_;
179	}
180	/** Returns the number of local rigid bodies */
181	unsigned int getNRigidBodies() {
182	return nRigidBodies_;
183	}
184
185	/** Returns the number of local integrable objects */
186	unsigned int getNIntegrableObjects() {
187	return nIntegrableObjects_;
188	}
189
190	/** Returns the number of local cutoff groups */
191	unsigned int getNCutoffGroups() {
192	return nCutoffGroups_;
193	}
194
195	/** Returns the total number of constraints in this SimInfo */
196	unsigned int getNConstraints() {
197	return nConstraints_;
198	}
199
200	/**
201	* Returns the first molecule in this SimInfo and intialize the iterator.
202	* @return the first molecule, return NULL if there is not molecule in this SimInfo
203	* @param i the iterator of molecule array (user shouldn't change it)
204	*/
205	Molecule* beginMolecule(MoleculeIterator& i);
206
207	/**
208	* Returns the next avaliable Molecule based on the iterator.
209	* @return the next avaliable molecule, return NULL if reaching the end of the array
210	* @param i the iterator of molecule array
211	*/
212	Molecule* nextMolecule(MoleculeIterator& i);
213
214	/** Returns the number of degrees of freedom */
215	int getNdf() {
216	return ndf_ - getFdf();
217	}
218
219	/** Returns the number of raw degrees of freedom */
220	int getNdfRaw() {
221	return ndfRaw_;
222	}
223
224	/** Returns the number of translational degrees of freedom */
225	int getNdfTrans() {
226	return ndfTrans_;
227	}
228
229	/** sets the current number of frozen degrees of freedom */
230	void setFdf(int fdf) {
231	fdf_local = fdf;
232	}
233
234	int getFdf();
235
236	//getNZconstraint and setNZconstraint ruin the coherent of SimInfo class, need refactorying
237
238	/** Returns the total number of z-constraint molecules in the system */
239	int getNZconstraint() {
240	return nZconstraint_;
241	}
242
243	/**
244	* Sets the number of z-constraint molecules in the system.
245	*/
246	void setNZconstraint(int nZconstraint) {
247	nZconstraint_ = nZconstraint;
248	}
249
250	/** Returns the snapshot manager. */
251	SnapshotManager* getSnapshotManager() {
252	return sman_;
253	}
254
255	/** Sets the snapshot manager. */
256	void setSnapshotManager(SnapshotManager* sman);
257
258	/** Returns the force field */
259	ForceField* getForceField() {
260	return forceField_;
261	}
262
263	Globals* getSimParams() {
264	return simParams_;
265	}
266
267	/** Returns the velocity of center of mass of the whole system.*/
268	Vector3d getComVel();
269
270	/** Returns the center of the mass of the whole system.*/
271	Vector3d getCom();
272	/** Returns the center of the mass and Center of Mass velocity of the whole system.*/
273	void getComAll(Vector3d& com,Vector3d& comVel);
274
275	/** Returns intertia tensor for the entire system and system Angular Momentum.*/
276	void getInertiaTensor(Mat3x3d &intertiaTensor,Vector3d &angularMomentum);
277
278	/** Returns system angular momentum */
279	Vector3d getAngularMomentum();
280
281	/** Returns volume of system as estimated by an ellipsoid defined by the radii of gyration*/
282	void getGyrationalVolume(RealType &vol);
283	/** Overloaded version of gyrational volume that also returns det(I) so dV/dr can be calculated*/
284	void getGyrationalVolume(RealType &vol, RealType &detI);
285	/** main driver function to interact with fortran during the initialization and molecule migration */
286	void update();
287
288	/** Returns the local index manager */
289	LocalIndexManager* getLocalIndexManager() {
290	return &localIndexMan_;
291	}
292
293	int getMoleculeStampId(int globalIndex) {
294	//assert(globalIndex < molStampIds_.size())
295	return molStampIds_[globalIndex];
296	}
297
298	/** Returns the molecule stamp */
299	MoleculeStamp* getMoleculeStamp(int id) {
300	return moleculeStamps_[id];
301	}
302
303	/** Return the total number of the molecule stamps */
304	int getNMoleculeStamp() {
305	return moleculeStamps_.size();
306	}
307	/**
308	* Finds a molecule with a specified global index
309	* @return a pointer point to found molecule
310	* @param index
311	*/
312	Molecule* getMoleculeByGlobalIndex(int index) {
313	MoleculeIterator i;
314	i = molecules_.find(index);
315
316	return i != molecules_.end() ? i->second : NULL;
317	}
318
319	int getGlobalMolMembership(int id){
320	return globalMolMembership_[id];
321	}
322
323	RealType getRcut() {
324	return rcut_;
325	}
326
327	RealType getRsw() {
328	return rsw_;
329	}
330
331	RealType getList() {
332	return rlist_;
333	}
334
335	std::string getFinalConfigFileName() {
336	return finalConfigFileName_;
337	}
338
339	void setFinalConfigFileName(const std::string& fileName) {
340	finalConfigFileName_ = fileName;
341	}
342
343	std::string getRawMetaData() {
344	return rawMetaData_;
345	}
346	void setRawMetaData(const std::string& rawMetaData) {
347	rawMetaData_ = rawMetaData;
348	}
349
350	std::string getDumpFileName() {
351	return dumpFileName_;
352	}
353
354	void setDumpFileName(const std::string& fileName) {
355	dumpFileName_ = fileName;
356	}
357
358	std::string getStatFileName() {
359	return statFileName_;
360	}
361
362	void setStatFileName(const std::string& fileName) {
363	statFileName_ = fileName;
364	}
365
366	std::string getRestFileName() {
367	return restFileName_;
368	}
369
370	void setRestFileName(const std::string& fileName) {
371	restFileName_ = fileName;
372	}
373
374	/**
375	* Sets GlobalGroupMembership
376	* @see #SimCreator::setGlobalIndex
377	*/
378	void setGlobalGroupMembership(const std::vector<int>& globalGroupMembership) {
379	assert(globalGroupMembership.size() == static_cast<size_t>(nGlobalAtoms_));
380	globalGroupMembership_ = globalGroupMembership;
381	}
382
383	/**
384	* Sets GlobalMolMembership
385	* @see #SimCreator::setGlobalIndex
386	*/
387	void setGlobalMolMembership(const std::vector<int>& globalMolMembership) {
388	assert(globalMolMembership.size() == static_cast<size_t>(nGlobalAtoms_));
389	globalMolMembership_ = globalMolMembership;
390	}
391
392
393	bool isFortranInitialized() {
394	return fortranInitialized_;
395	}
396
397	bool getCalcBoxDipole() {
398	return calcBoxDipole_;
399	}
400
401	bool getUseAtomicVirial() {
402	return useAtomicVirial_;
403	}
404
405	//below functions are just forward functions
406	//To compose or to inherit is always a hot debate. In general, is-a relation need subclassing, in the
407	//the other hand, has-a relation need composing.
408	/**
409	* Adds property into property map
410	* @param genData GenericData to be added into PropertyMap
411	*/
412	void addProperty(GenericData* genData);
413
414	/**
415	* Removes property from PropertyMap by name
416	* @param propName the name of property to be removed
417	*/
418	void removeProperty(const std::string& propName);
419
420	/**
421	* clear all of the properties
422	*/
423	void clearProperties();
424
425	/**
426	* Returns all names of properties
427	* @return all names of properties
428	*/
429	std::vector<std::string> getPropertyNames();
430
431	/**
432	* Returns all of the properties in PropertyMap
433	* @return all of the properties in PropertyMap
434	*/
435	std::vector<GenericData*> getProperties();
436
437	/**
438	* Returns property
439	* @param propName name of property
440	* @return a pointer point to property with propName. If no property named propName
441	* exists, return NULL
442	*/
443	GenericData* getPropertyByName(const std::string& propName);
444
445	/**
446	* add all special interaction pairs (including excluded
447	* interactions) in a molecule into the appropriate lists.
448	*/
449	void addInteractionPairs(Molecule* mol);
450
451	/**
452	* remove all special interaction pairs which belong to a molecule
453	* from the appropriate lists.
454	*/
455	void removeInteractionPairs(Molecule* mol);
456
457
458	/** Returns the unique atom types of local processor in an array */
459	std::set<AtomType*> getUniqueAtomTypes();
460
461	friend std::ostream& operator <<(std::ostream& o, SimInfo& info);
462
463	void getCutoff(RealType& rcut, RealType& rsw);
464
465	private:
466
467	/** fill up the simtype struct*/
468	void setupSimType();
469
470	/**
471	* Setup Fortran Simulation
472	* @see #setupFortranParallel
473	*/
474	void setupFortranSim();
475
476	/** Figure out the radius of cutoff, radius of switching function and pass them to fortran */
477	void setupCutoff();
478
479	/** Figure out which coulombic correction method to use and pass to fortran */
480	void setupElectrostaticSummationMethod( int isError );
481
482	/** Figure out which polynomial type to use for the switching function */
483	void setupSwitchingFunction();
484
485	/** Determine if we need to accumulate the simulation box dipole */
486	void setupAccumulateBoxDipole();
487
488	/** Calculates the number of degress of freedom in the whole system */
489	void calcNdf();
490	void calcNdfRaw();
491	void calcNdfTrans();
492
493	ForceField* forceField_;
494	Globals* simParams_;
495
496	std::map<int, Molecule> molecules_; /< Molecule array /
497
498	/**
499	* Adds molecule stamp and the total number of the molecule with same molecule stamp in the whole
500	* system.
501	*/
502	void addMoleculeStamp(MoleculeStamp* molStamp, int nmol);
503
504	//degress of freedom
505	int ndf_; /*< number of degress of freedom (excludes constraints), ndf_ is local /
506	int fdf_local; /*< number of frozen degrees of freedom /
507	int fdf_; /*< number of frozen degrees of freedom /
508	int ndfRaw_; /*< number of degress of freedom (includes constraints), ndfRaw_ is local /
509	int ndfTrans_; /*< number of translation degress of freedom, ndfTrans_ is local /
510	int nZconstraint_; /** number of z-constraint molecules, nZconstraint_ is global */
511
512	//number of global objects
513	int nGlobalMols_; /*< number of molecules in the system /
514	int nGlobalAtoms_; /*< number of atoms in the system /
515	int nGlobalCutoffGroups_; /*< number of cutoff groups in this system /
516	int nGlobalIntegrableObjects_; /*< number of integrable objects in this system /
517	int nGlobalRigidBodies_; /*< number of rigid bodies in this system /
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 cutoff group this atom belong to.
521	* It is filled by SimCreator once and only once, since it never changed during the simulation.
522	*/
523	std::vector<int> globalGroupMembership_;
524
525	/**
526	* the size of globalMolMembership_ is nGlobalAtoms. Its index is global index of an atom, and the
527	* corresponding content is the global index of molecule this atom belong to.
528	* It is filled by SimCreator once and only once, since it is never changed during the simulation.
529	*/
530	std::vector<int> globalMolMembership_;
531
532
533	std::vector<int> molStampIds_; /*< stamp id array of all molecules in the system /
534	std::vector<MoleculeStamp> moleculeStamps_; /< molecule stamps array /
535
536	//number of local objects
537	int nAtoms_; /*< number of atoms in local processor /
538	int nBonds_; /*< number of bonds in local processor /
539	int nBends_; /*< number of bends in local processor /
540	int nTorsions_; /*< number of torsions in local processor /
541	int nInversions_; /*< number of inversions in local processor /
542	int nRigidBodies_; /*< number of rigid bodies in local processor /
543	int nIntegrableObjects_; /*< number of integrable objects in local processor /
544	int nCutoffGroups_; /*< number of cutoff groups in local processor /
545	int nConstraints_; /*< number of constraints in local processors /
546
547	simtype fInfo_; /*< A dual struct shared by c++/fortran which indicates the atom types in simulation/
548	PairList excludedInteractions_;
549	PairList oneTwoInteractions_;
550	PairList oneThreeInteractions_;
551	PairList oneFourInteractions_;
552	PropertyMap properties_; /*< Generic Property /
553	SnapshotManager* sman_; /*< SnapshotManager /
554
555	/**
556	* The reason to have a local index manager is that when molecule is migrating to other processors,
557	* the atoms and the rigid-bodies will release their local indices to LocalIndexManager. Combining the
558	* information of molecule migrating to current processor, Migrator class can query the LocalIndexManager
559	* to make a efficient data moving plan.
560	*/
561	LocalIndexManager localIndexMan_;
562
563	// unparsed MetaData block for storing in Dump and EOR files:
564	std::string rawMetaData_;
565
566	//file names
567	std::string finalConfigFileName_;
568	std::string dumpFileName_;
569	std::string statFileName_;
570	std::string restFileName_;
571
572	RealType rcut_; /*< cutoff radius/
573	RealType rsw_; /*< radius of switching function/
574	RealType rlist_; /*< neighbor list radius /
575
576	int ljsp_; /*< use shifted potential for LJ/
577	int ljsf_; /*< use shifted force for LJ/
578
579	bool fortranInitialized_; /** flag to indicate whether the fortran side is initialized */
580
581	bool calcBoxDipole_; /**< flag to indicate whether or not we calculate
582	the simulation box dipole moment */
583
584	bool useAtomicVirial_; /**< flag to indicate whether or not we use
585	Atomic Virials to calculate the pressure */
586
587	public:
588	/**
589	* return an integral objects by its global index. In MPI version, if the StuntDouble with specified
590	* global index does not belong to local processor, a NULL will be return.
591	*/
592	StuntDouble* getIOIndexToIntegrableObject(int index);
593	void setIOIndexToIntegrableObject(const std::vector<StuntDouble*>& v);
594	private:
595	std::vector<StuntDouble*> IOIndexToIntegrableObject;
596	//public:
597	//void setStuntDoubleFromGlobalIndex(std::vector<StuntDouble*> v);
598	/**
599	* return a StuntDouble by its global index. In MPI version, if the StuntDouble with specified
600	* global index does not belong to local processor, a NULL will be return.
601	*/
602	//StuntDouble* getStuntDoubleFromGlobalIndex(int index);
603	//private:
604	//std::vector<StuntDouble*> sdByGlobalIndex_;
605
606	//in Parallel version, we need MolToProc
607	public:
608
609	/**
610	* Finds the processor where a molecule resides
611	* @return the id of the processor which contains the molecule
612	* @param globalIndex global Index of the molecule
613	*/
614	int getMolToProc(int globalIndex) {
615	//assert(globalIndex < molToProcMap_.size());
616	return molToProcMap_[globalIndex];
617	}
618
619	/**
620	* Set MolToProcMap array
621	* @see #SimCreator::divideMolecules
622	*/
623	void setMolToProcMap(const std::vector<int>& molToProcMap) {
624	molToProcMap_ = molToProcMap;
625	}
626
627	private:
628
629	void setupFortranParallel();
630
631	/**
632	* The size of molToProcMap_ is equal to total number of molecules
633	* in the system. It maps a molecule to the processor on which it
634	* resides. it is filled by SimCreator once and only once.
635	*/
636	std::vector<int> molToProcMap_;
637
638
639	};
640
641	} //namespace OpenMD
642	#endif //BRAINS_SIMMODEL_HPP
643